Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Ye, Y.
Right arrow Articles by Godzik, A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Ye, Y.
Right arrow Articles by Godzik, A.
Social Bookmarking
 Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 19 Suppl. 2 2003
pages ii246-ii255
© 2003 Oxford University Press

Flexible structure alignment by chaining aligned fragment pairs allowing twists

Yuzhen Ye and Adam Godzik *

Program in Bioinformatics and Systems Biology, The Burnham Institute, La Jolla, CA 92037, USA

Received on March 17, 2003 ; accepted on June 9, 2003

Motivation: Protein structures are flexible and undergo structural rearrangements as part of their function, and yet most existing protein structure comparison methods treat them as rigid bodies, which may lead to incorrect alignment.

Results: We have developed the Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT), a new method for structural alignment of proteins. The FATCAT approach simultaneously addresses the two major goals of flexible structure alignment; optimizing the alignment and minimizing the number of rigid-body movements (twists) around pivot points (hinges) introduced in the reference protein. In contrast, currently existing flexible structure alignment programs treat the hinge detection as a post-process of a standard rigid body alignment. We illustrate the advantages of the FATCAT approach by several examples of comparison between proteins known to adopt different conformations, where the FATCAT algorithm achieves more accurate structure alignments than current methods, while at the same time introducing fewer hinges.

Contacts: adam{at}burnham.org

* To whom correspondence should be addressed.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
Nucleic Acids ResHome page
A. Nigham, L. Tucker-Kellogg, I. Mihalek, C. Verma, and D. Hsu
pFlexAna: detecting conformational changes in remotely related proteins
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W246 - W251.
[Abstract] [Full Text] [PDF]


Home page
Appl. Environ. Microbiol.Home page
T. Tsukihara, Y. Honda, R. Sakai, T. Watanabe, and T. Watanabe
Mechanism for Oxidation of High-Molecular-Weight Substrates by a Fungal Versatile Peroxidase, MnP2
Appl. Envir. Microbiol., May 1, 2008; 74(9): 2873 - 2881.
[Abstract] [Full Text] [PDF]


Home page
Protein Sci.Home page
P. L. Hayes, B. L. Lytle, B. F. Volkman, and F. C. Peterson
The solution structure of ZNF593 from Homo sapiens reveals a zinc finger in a predominately unstructured protein
Protein Sci., March 1, 2008; 17(3): 571 - 576.
[Abstract] [Full Text] [PDF]


Home page
J. Immunol.Home page
M. Occhino, F. Ghiotto, S. Soro, M. Mortarino, S. Bosi, M. Maffei, S. Bruno, M. Nardini, M. Figini, A. Tramontano, et al.
Dissecting the Structural Determinants of the Interaction between the Human Cytomegalovirus UL18 Protein and the CD85j Immune Receptor
J. Immunol., January 15, 2008; 180(2): 957 - 968.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
J. S. Dias, A. L. Macedo, G. C. Ferreira, F. C. Peterson, B. F. Volkman, and B. J. Goodfellow
The First Structure from the SOUL/HBP Family of Heme-binding Proteins, Murine P22HBP
J. Biol. Chem., October 20, 2006; 281(42): 31553 - 31561.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
Y. Ye and A. Godzik
Multiple flexible structure alignment using partial order graphs
Bioinformatics, May 15, 2005; 21(10): 2362 - 2369.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
B. L. Lytle, F. C. Peterson, S.-H. Qiu, M. Luo, Q. Zhao, J. L. Markley, and B. F. Volkman
Solution Structure of a Ubiquitin-like Domain from Tubulin-binding Cofactor B
J. Biol. Chem., November 5, 2004; 279(45): 46787 - 46793.
[Abstract] [Full Text] [PDF]


Home page
Protein Sci.Home page
Y. Ye and A. Godzik
Database searching by flexible protein structure alignment
Protein Sci., July 1, 2004; 13(7): 1841 - 1850.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
Y. Ye and A. Godzik
FATCAT: a web server for flexible structure comparison and structure similarity searching
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W582 - W585.
[Abstract] [Full Text] [PDF]



Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.